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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTGCCACTCTACATGAAGCTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttaccagttaccaagctcttttaggcttttgcaccgtttcttttaatttcttgttcttatatttgcttgttcctttttatacaattttttcaataaaaaagaaggaattgcatgtagccaactgtgagacctcaataaattctgcag

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 18
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|6952479|gb|AW424547.1|AW424547
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|113703092|gb|EE680596.1|EE680596
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60353902|gb|DN220875.1|DN220875
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|211228557|gb|FL433549.1|FL433549
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60398537|gb|DN231353.1|DN231353
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|211470957|gb|FL472665.1|FL472665
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60338498|gb|DN205471.1|DN205471
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|33098241|gb|CF058201.1|CF058201
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|149089739|gb|EE179010.2|EE179010
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|78092216|gb|DV520590.1|DV520590
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|4314687|gb|AI438596.2|AI438596
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60339876|gb|DN206849.1|DN206849
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60339654|gb|DN206627.1|DN206627
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|211470956|gb|FL472664.1|FL472664
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGMCAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|37388666|gb|CF631544.1|CF631544
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|211228558|gb|FL433550.1|FL433550
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|5069904|gb|AI737869.1|AI737869
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|16378424|gb|BI992438.1|BI992438
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|13249712|gb|BG360617.1|BG360617
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60346740|gb|DN213713.1|DN213713
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|211478697|gb|FL031225.1|FL031225
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTC
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTC
EST: gi|8665943|gb|BE186759.1|BE186759
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|76021643|gb|DT948813.1|DT948813
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACCGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|211478698|gb|FL031226.1|FL031226
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTA
EST: gi|78544270|gb|DV621768.1|DV621768
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60338142|gb|DN205115.1|DN205115
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60344806|gb|DN211779.1|DN211779
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|50334017|gb|CO529143.1|CO529143
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGCCAGGCCAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTCCATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
EST: gi|60343958|gb|DN210931.1|DN210931
EST:     CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAG                         GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA
genomic: CTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 131

GTTCTTGCCACTCTACATGAAGCTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 100

GTTCTTGCCACTCTACATGAAGCTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

GTTCTTGCCACTCTACATGAAGCTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

GTTCTTGCCACTCTACATGAAGCTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttacca ... aattctgcagGTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTGCCACTCTACATGAAGCTGGTTTTCATGTTGATATTGACGCGAGTGACAGGACAATACAAAAGAAGgtacttaccagttaccaagctcttttaggcttttgcaccgtttcttttaatttcttgttcttatatttgcttgttcctttttatacaattttttcaataaaaaagaaggaattgcatgtagccaactgtgagacctcaataaattctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG